rs7091875

chr10-22741353-G-Achr10-22741353-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.358 in 151,838 control chromosomes in the GnomAD database, including 10,658 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10658 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54333 AN: 151720 Hom.: 10647 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 54381 AN: 151838 Hom.: 10658 Cov.: 31 AF XY: 0.350 AC XY: 25986 AN XY: 74176

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.376

Alfa AF: 0.319 Hom.: 12115

Bravo AF: 0.366

Asia WGS AF: 0.265 AC: 921 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7091875; hg19: chr10-23030282;